What happens if a registered person has paid IGST on a transaction considered by him to be an inter-state supply but which is subsequently held to be an intra-state supply

Refund of IGST (in IGST Act) shall be granted in such manner and subject to such conditions as may be prescribed.

(ICAI FAQ PUBLICATIONS 06-09-2017 Tax wrongfully collected and paid to Central Government or State Government : FAQ NO. 37)